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1. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Author

Maura Costello, Mark Fleharty, Justin Abreu, Yossi Farjoun, Steven Ferriera, Laurie Holmes, Brian Granger, Lisa Green, Tom Howd, Tamara Mason, Gina Vicente, Michael Dasilva, Wendy Brodeur, Timothy DeSmet, Sheila Dodge, Niall J. Lennon, and Stacey Gabriel

Subjects
Next generation sequencing, Massively parallel sequencing, ILLUMINA sequencing, Index swapping, Index hopping, Multiplexing, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification (ExAmp) chemistry (HiSeqX, HiSeq4000, and NovaSeq). We also present a remediation method that minimizes the impact of such swaps. Results Leveraging data collected over a two-year period, we demonstrate the widespread prevalence of index swapping in patterned flow cell data. We calculate mean swap rates across multiple sample preparation methods and sequencer models, demonstrating that different library methods can have vastly different swapping rates and that even non-ExAmp chemistry instruments display trace levels of index swapping. We provide methods for eliminating sample data cross contamination by utilizing non-redundant dual indexing for complete filtering of index swapped reads, and share the sequences for 96 non-combinatorial dual indexes we have validated across various library preparation methods and sequencer models. Finally, using computational methods we provide a greater insight into the mechanism of index swapping. Conclusions Index swapping in pooled libraries is a prevalent phenomenon that we observe at a rate of 0.2 to 6% in all sequencing runs on HiSeqX, HiSeq 4000/3000, and NovaSeq. Utilizing non-redundant dual indexing allows for the removal (flagging/filtering) of these swapped reads and eliminates swapping induced sample contamination, which is critical for sensitive applications such as RNA-seq, single cell, blood biopsy using circulating tumor DNA, or clinical sequencing.

Published
2018
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2. Returning integrated genomic risk and clinical recommendations: the eMERGE study

Author

Jodell E. Linder, Aimee Allworth, Sarah T. Bland, Pedro J. Caraballo, Rex L. Chisholm, Ellen Wright Clayton, David R. Crosslin, Ozan Dikilitas, Alanna DiVietro, Edward D. Esplin, Sophie Forman, Robert R. Freimuth, Adam S. Gordon, Richard Green, Maegan V. Harden, Ingrid A. Holm, Gail P. Jarvik, Elizabeth W. Karlson, Sofia Labrecque, Niall J. Lennon, Nita A. Limdi, Kathleen F. Mittendorf, Shawn N. Murphy, Lori Orlando, Cynthia A. Prows, Luke V. Rasmussen, Laura Rasmussen-Torvik, Robb Rowley, Konrad Teodor Sawicki, Tara Schmidlen, Shannon Terek, David Veenstra, Digna R. Velez Edwards, Devin Absher, Noura S. Abul-Husn, Jorge Alsip, Hana Bangash, Mark Beasley, Jennifer E. Below, Eta S. Berner, James Booth, Wendy K. Chung, James J. Cimino, John Connolly, Patrick Davis, Beth Devine, Stephanie M. Fullerton, Candace Guiducci, Melissa L. Habrat, Heather Hain, Hakon Hakonarson, Margaret Harr, Eden Haverfield, Valentina Hernandez, Christin Hoell, Martha Horike-Pyne, George Hripcsak, Marguerite R. Irvin, Christopher Kachulis, Dean Karavite, Eimear E. Kenny, Atlas Khan, Krzysztof Kiryluk, Bruce Korf, Leah Kottyan, Iftikhar J. Kullo, Katie Larkin, Cong Liu, Edyta Malolepsza, Teri A. Manolio, Thomas May, Elizabeth M. McNally, Frank Mentch, Alexandra Miller, Sean D. Mooney, Priyanka Murali, Brenda Mutai, Naveen Muthu, Bahram Namjou, Emma F. Perez, Megan J. Puckelwartz, Tejinder Rakhra-Burris, Dan M. Roden, Elisabeth A. Rosenthal, Seyedmohammad Saadatagah, Maya Sabatello, Dan J. Schaid, Baergen Schultz, Lynn Seabolt, Gabriel Q. Shaibi, Richard R. Sharp, Brian Shirts, Maureen E. Smith, Jordan W. Smoller, Rene Sterling, Sabrina A. Suckiel, Jeritt Thayer, Hemant K. Tiwari, Susan B. Trinidad, Theresa Walunas, Wei-Qi Wei, Quinn S. Wells, Chunhua Weng, Georgia L. Wiesner, Ken Wiley, Josh F. Peterson, Adam Gordon, Agboade Sobowale, Akshar Patel, Alanna Strong, Alborz Sherafati, Alborz Sherfati, Alex Bick, Alka Chandel, Alyssa Rosenthal, Amit Khera, Amy Kontorovich, Andrew Beck, Andy Beck, Angelica Espinoza, Anna Lewis, Anya Prince, Ayuko Iverson, Bahram Namjou Khales, Barbara Benoit, Becca Hernan, Ben Kallman, Ben Kerman, Ben Shoemaker, Benjamin Satterfield, Bethany Etheridge, Blake Goff, Bob Freimuth, Bob Grundmeier, Brenae Collier, Brett Harnett, Brian Chang, Brian Piening, Brittney Davis, Candace Patterson, Carmen Demetriou, Casey Ta, Catherine Hammack, Catrina Nelson, Caytie Gascoigne, Chad Dorn, Chad Moretz, Chris Kachulis, Christie Hoell, Christine Cowles, Christoph Lange, Cindy Prows, Cole Brokamp, Courtney Scherr, Crystal Gonzalez, Cynthia Ramirez, Daichi Shimbo, Dan Roden, Daniel Schaid, Dave Kaufman, David Crosslin, David Kochan, Davinder Singh, Debbie Abrams, Digna Velez Edwards, Eduardo Morales, Edward Esplin, Ehsan Alipour, Eimear Kenny, Elisabeth Rosenthal, Eliza Duvall, Elizabeth McNally, Elizabeth Bhoj, Elizabeth Cohn, Elizabeth Hibler, Elizabeth Karlson, Ellen Clayton, Emily Chesnut, Emily DeFranco, Emily Gallagher, Emily Soper, Emma Perez, Erin Cash, Eta Berner, Fei Wang, Firas Wehbe, Francisco Ricci, Gabriel Shaibi, Gail Jarvik, George Hahn, Georgia Wiesner, Gillian Belbin, Gio Davogustto, Girish Nadkarni, Haijun Qiu, Hannah Beasley, Hao Liu, Heide Aungst, Hemant Tiwari, Hillary Duckham, Hope Thomas, Iftikhar Kullo, Ingrid Holm, Isabelle Allen, Iuliana Ionita-Laza, Jacklyn Hellwege, Jacob Petrzelka, Jacqueline Odgis, Jahnavi Narula, Jake Petrzelka, Jalpa Patel, James Cimino, James Meigs, James Snyder, Janet Olson, Janet Zahner, Jeff Pennington, Jen Pacheco, Jennifer Allen Pacheco, Jennifer Morse, Jeremy Corsmo, Jim Cimino, Jingheng Chen, Jocelyn Fournier, Jodell Jackson, Joe Glessner, Joel Pacyna, Johanna Smith, John Lynch, John Shelley, Jonathan Mosley, Jordan Nestor, Jordan Smoller, Joseph Kannry, Joseph Sutton, Josh Peterson, Joshua Smith, Julia Galasso, Julia Smith, Julia Wynn, Justin Gundelach, Justin Starren, Karmel Choi, Kate Mittendorf, Katherine Anderson, Katherine Bonini, Kathleen Leppig, Kathleen Muenzen, Kelsey Stuttgen, Kenny Nguyen, Kevin Dufendach, Kiley Atkins, Konrad Sawicki, Kristjan Norland, Laura Beskow, Li Hsu, Lifeng Tian, Lisa Mahanta, Lisa Martin, Lisa Wang, Lizbeth Gomez, Lorenzo Thompson, Lucas Richter, Luke Rasmussen, Lynn Petukhova, Madison O’Brien, Maegan Harden, Malia Fullerton, Marta Guindo, Martha Horike, Marwah Abdalla, Marwan Hamed, Mary Beth Terry, Mary Maradik, Matt Wyatt, Matthew Davis, Matthew Lebo, Maureen Smith, Maya del Rosario, Meckenzie Behr, Meg Roy-Puckelwartz, Mel Habrat, Melanie Myers, Meliha Yetisgen, Merve Iris, Michael DaSilva, Michael Preuss, Michelle McGowan, Mingjian Shi, Minoli Perera, Minta Thomas, Mitch Elkind, Mohammad Abbass, Mohammad Saadatagah, Molly Hess, Molly Maradik, Nataraja 'RJ' Vaitinadin, Nataraja Vaitinadin, Neil Netherly, Niall Lennon, Ning Shang, Nita Limdi, Noah Forrest, Noheli Romero, Nora Robinson, Noura Abul-Husn, Omar Elsekaily, Patricia Kovatch, Paul Appelbaum, Paul Francaviglia, Paul O’Reilly, Paulette Chandler, Pedro Caraballo, Peter Tarczy-Hornoch, Pierre Shum, Priya Marathe, Qiping Feng, Quinn Wells, Rachel Atchley, Radhika Narla, Rene Barton, Rex Chisholm, Richard Sharp, Riki Peters, Rita Kukafka, Robert Freimuth, Robert Green, Robert Winter, Roger Mueller, Ruth Loos, Ryan Irvin, Sabrina Suckiel, Sajjad Hussain, Samer Sharba, Sandy Aronson, Sarah Jones, Sarah Knerr, Scott Nigbur, Scott Weiss, Sean Mooney, Sharon Aufox, Sharon Nirenberg, Shawn Murphy, Sheila O’Byrne, Shing Wang (Sam) Choi, Sienna Aguilar, S.T. Bland, Stefanie Rodrigues, Stephanie Ledbetter, Stephanie Rutledge, Stuart James Booth, Su Xian, Susan Brown Trinidad, Suzanne Bakken, Teri Manolio, Tesfaye Mersha, Thevaa Chandereng, Tian Ge, Todd Edwards, Tom Kaszemacher, Valerie Willis, Vemi Desai, Vimi Desai, Virginia Lorenzi, Vivian Gainer, Wendy Chung, Wu-Chen Su, Xiao Chang, Yiqing Zhao, Yuan Luo, and Yufeng Shen

Subjects
Genetics (clinical)
Abstract

Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk.To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores (PRS), monogenic risks, family history, and clinical risk assessments via a Genome Informed Risk Assessment (GIRA) report and will assess uptake of care recommendations after return of results.GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022.Return of a novel report for communicating monogenic, polygenic, and family history based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.

Published
2022

4. The Potential and Limitations of Diatoms as Environmental Indicators in Mid-Atlantic Coastal Wetlands

Author

Elizabeth Burke Watson, Marina Potapova, Daniel R Millemann, Lee Lippincott, Nina Desianti, Mihaela D. Enache, Michael DaSilva, Ksawery J. Biskup, Austin Degen, Michael L. Griffiths, Andrew B. Gray, and Daria Nikitina

Subjects
0106 biological sciences, geography, Marsh, geography.geographical_feature_category, 010504 meteorology & atmospheric sciences, Ecology, biology, 010604 marine biology & hydrobiology, Marine habitats, Intertidal zone, Wetland, Aquatic Science, biology.organism_classification, 01 natural sciences, Oceanography, Diatom, Benthic zone, Nutrient pollution, Salt marsh, Environmental science, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences
Abstract

Diatoms have been successfully used as indicators of past and present environmental conditions in freshwater and marine habitats, but their diversity and indicative properties in microtidal coastal wetlands of temperate zone are relatively poorly studied. The goal of this study was to determine whether diatoms can be used as indicators of sea level and nutrient content in coastal wetlands of the mid-Atlantic region of the USA. Our exploratory analyses indicated that benthic and marsh soil diatom assemblages were jointly controlled by tidal elevation, salinity, sediment texture, and nutrient content, while the relative importance of these factors varied among datasets targeting different environmental gradients. The habitat type could be correctly inferred from diatom assemblage composition in 79% of samples. A diatom-based model developed for inferring sediment nitrogen content had an average accuracy of prediction of 12.5% of observed nitrogen range. Models for inferring tidal exposure from diatom assemblage data provided assessment with 11–16% accuracy as estimated by the bootstrapped root mean square errors of prediction, which is similar to the accuracy of models based on other microfossils. These results show that despite inherent challenges, such as tidal redistribution of diatom frustules across the intertidal zone, diatoms can be successfully used as an independent source of evidence in paleoreconstructions of sea-level change and nitrogen enrichment, as well as for monitoring current nutrient pollution in mid-Atlantic wetlands.

Published
2019
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5. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Author

Brian E. Granger, Steven Ferriera, Stacey Gabriel, Mark Fleharty, Sheila Dodge, Tom Howd, Justin Abreu, Yossi Farjoun, Wendy Brodeur, Lisa Green, Tamara Mason, Niall J. Lennon, Timothy DeSmet, Laurie Holmes, Michael Dasilva, Maura Costello, and Gina Vicente

Subjects
0301 basic medicine, animal structures, Massively parallel sequencing, lcsh:QH426-470, Computer science, lcsh:Biotechnology, Parallel computing, environment and public health, Multiplexing, DNA sequencing, 03 medical and health sciences, Next generation sequencing, lcsh:TP248.13-248.65, Genetics, Humans, Illumina dye sequencing, Gene Library, Exclusion amplification, Massive parallel sequencing, Genome, Human, Flagging, fungi, Search engine indexing, High-Throughput Nucleotide Sequencing, Indexes, DNA, Sequence Analysis, DNA, Sample (graphics), Index hopping, Index, lcsh:Genetics, 030104 developmental biology, Index (publishing), Index swapping, Barcodes, ILLUMINA sequencing, Sequence Analysis, Research Article, Biotechnology
Abstract

Background Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification (ExAmp) chemistry (HiSeqX, HiSeq4000, and NovaSeq). We also present a remediation method that minimizes the impact of such swaps. Results Leveraging data collected over a two-year period, we demonstrate the widespread prevalence of index swapping in patterned flow cell data. We calculate mean swap rates across multiple sample preparation methods and sequencer models, demonstrating that different library methods can have vastly different swapping rates and that even non-ExAmp chemistry instruments display trace levels of index swapping. We provide methods for eliminating sample data cross contamination by utilizing non-redundant dual indexing for complete filtering of index swapped reads, and share the sequences for 96 non-combinatorial dual indexes we have validated across various library preparation methods and sequencer models. Finally, using computational methods we provide a greater insight into the mechanism of index swapping. Conclusions Index swapping in pooled libraries is a prevalent phenomenon that we observe at a rate of 0.2 to 6% in all sequencing runs on HiSeqX, HiSeq 4000/3000, and NovaSeq. Utilizing non-redundant dual indexing allows for the removal (flagging/filtering) of these swapped reads and eliminates swapping induced sample contamination, which is critical for sensitive applications such as RNA-seq, single cell, blood biopsy using circulating tumor DNA, or clinical sequencing. Electronic supplementary material The online version of this article (10.1186/s12864-018-4703-0) contains supplementary material, which is available to authorized users.

Published
2018
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6. The Pluralist Right to Health Care : A Framework and Case Study

Author

Michael DaSilva and Michael DaSilva

Subjects
Right to health--Canada
Abstract

Health rights are a common but controversial legal phenomenon. Every country is signatory to a treaty that incorporates health rights, yet existing health rights do not fit easily into the traditional'claim right'model, and questions remain over how to theoretically incorporate health rights into domestic systems. The Pluralist Right to Health Care addresses this incongruity between theory and practice with an account of the right to health care that is both philosophically and practically sound. Utilizing a pluralist framework, Michael Da Silva argues that the right to health care is best understood as a set of claims to related ends: the goods necessary for a dignified existence, procedural fairness in determining what other goods to provide and in the provision of goods, and a functioning health care system. Through philosophical reasoning, analysis of relevant international human rights law, and a close study of the Canadian case, The Pluralist Right to Health Care provides crucial insight into the potential of law and policy to improve health care systems in Canada and beyond.

Published
2021

8. A 4000-YEAR ENVIRONMENTAL EVALUATION OF MID-ATLANTIC COASTAL WETLANDS FROM PAIRED GEOCHEMICAL AND DIATOM ANALYSIS OF SURFICIAL AND DOWN-CORE SEDIMENTS

Author

Mihaela D. Enache, Michael DaSilva, Nina Desianti, Ksawery J. Biskup, Marina Potapova, Austin Degen, Rob Tunstead, Michael L. Griffiths, and David Steinmann

Subjects
Core (optical fiber), geography, geography.geographical_feature_category, Oceanography, Diatom, Environmental evaluation, biology, Wetland, biology.organism_classification, Geology
Published
2019
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12. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Author

Tom Howd, Yossi Farjoun, Tamara Mason, Niall J. Lennon, Maura Costello, Timothy DeSmet, Michael Dasilva, Stacey Gabriel, Sheila Dodge, Gina Vicente, Wendy Brodeur, Laurie Holmes, Mark Fleharty, Justin Abreu, and Steven Ferriera

Subjects
Massive parallel sequencing, Index (publishing), Data integrity, Search engine indexing, Parallel computing, DUAL (cognitive architecture), Interest rate swap, Sample (graphics), TRACE (psycholinguistics)
Abstract

Here, we present an in-depth characterization of the index swapping mechanism on Illumina instruments that employ the ExAmp chemistry for cluster generation (HiSeqX, HiSeq4000, and NovaSeq). We discuss best practices for eliminating the effects of index swapping on data integrity by utilizing unique dual indexing for complete filtering of index swapped reads. We calculate mean swap rates across multiple sample preparation methods and sequencer models, demonstrating that different methods can have vastly different swap rates, and show that even non-ExAmp chemistry instruments display trace levels of index swapping. Finally, using computational methods we provide a greater insight into the mechanism of index swapping.

Published
2017
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15. Fetal rhesus monkey model of obstructive renal dysplasia

Author

Douglas G. Matsell, Alice F. Tarantal, Kent C. Cochrum, Michael Dasilva, Victor K.M. Han, and Amy Mok

Subjects
Pathology, medicine.medical_specialty, congenital obstructive uropathy, 030232 urology & nephrology, Kidney development, Apoptosis, Nephron, urologic and male genital diseases, Kidney, Ultrasonography, Prenatal, End stage renal disease, 03 medical and health sciences, Embryonic and Fetal Development, 0302 clinical medicine, Fetus, ultrasound techniques, Medicine, Animals, pediatric kidney failure, Obstructive uropathy, podocyte injury, 030304 developmental biology, 0303 health sciences, end-stage renal disease, business.industry, medicine.disease, Renal dysplasia, Macaca mulatta, kidney failure, Disease Models, Animal, medicine.anatomical_structure, Dysplasia, Nephrology, Female, business, Cell Division, Kidney disease, Ureteral Obstruction
Abstract

Fetal rhesus monkey model of obstructive renal dysplasia. Background Disorders of kidney development represent a major cause of renal failure and end-stage renal disease in the pediatric population. To understand further the prenatal pathogenesis of obstructive renal dysplasia, a fetal monkey model was developed using ultrasound-guided techniques. Methods Ureteropelvic obstruction ( N = 13) was induced during the early or late second trimester by the injection of purified guluronic alginate spheres. All fetuses were monitored sonographically, and then fetal tissues were removed at varying time points during the second and third trimesters. Results There was no evidence of oligohydramnios during the course of gestation, and the obstructed kidneys were typically progressively smaller than the contralateral (nonobstructed) kidneys when monitored sonographically over time. Obstructed kidneys displayed most features of renal dysplasia, including numerous cortical cysts of various sizes derived predominantly from collecting ducts and glomeruli. Mesenchymal changes included expansion of both the cortical and medullary interstitium, as well as mesenchymal-myocyte transformation, expressed as pericystic and peritubular fibromuscular collar formation. An important feature of this model was the disruption of normal glomerular development and architecture, associated with significant podocyte apoptosis, evident as early as the prevascularized S-shaped nephron. As in other models, collecting duct cell apoptosis was apparent, particularly in areas of cyst formation and cellular atrophy. Conclusions These results demonstrate the importance of this nonhuman primate model for exploring the pathophysiology of congenital obstructive uropathy and highlight the potential role of podocyte injury in determining long-term renal function associated with this condition.

Published
2001

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